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Diffstat (limited to 'var/spack/repos/builtin/packages/biopieces/package.py')
-rw-r--r-- | var/spack/repos/builtin/packages/biopieces/package.py | 70 |
1 files changed, 70 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/biopieces/package.py b/var/spack/repos/builtin/packages/biopieces/package.py new file mode 100644 index 0000000000..c237fdf564 --- /dev/null +++ b/var/spack/repos/builtin/packages/biopieces/package.py @@ -0,0 +1,70 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Biopieces(Package): + """The Biopieces are a collection of bioinformatics tools that can be + pieced together in a very easy and flexible manner to perform both + simple and complex tasks.""" + + homepage = "http://maasha.github.io/biopieces/" + git = "https://github.com/maasha/biopieces.git" + + version('2016-04-12', commit='982f80f7c55e2cae67737d80fe35a4e784762856', + submodules=True) + + depends_on('perl', type=('build', 'run')) + depends_on('perl-module-build', type=('build', 'run')) + depends_on('perl-bit-vector', type=('build', 'run')) + depends_on('perl-svg', type=('build', 'run')) + depends_on('perl-term-readkey', type=('build', 'run')) + depends_on('perl-time-hires', type=('build', 'run')) + depends_on('perl-dbi', type=('build', 'run')) + depends_on('perl-xml-parser', type=('build', 'run')) + depends_on('perl-carp-clan', type=('build', 'run')) + depends_on('perl-class-inspector', type=('build', 'run')) + depends_on('perl-html-parser', type=('build', 'run')) + depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-soap-lite', type=('build', 'run')) + depends_on('perl-uri', type=('build', 'run')) + depends_on('perl-inline', type=('build', 'run')) + depends_on('perl-inline-c', type=('build', 'run')) + depends_on('perl-parse-recdescent', type=('build', 'run')) + depends_on('perl-version', type=('build', 'run')) + depends_on('perl-dbfile', type=('build', 'run')) + depends_on('perl-dbd-mysql', type=('build', 'run')) + + depends_on('ruby@1.9:') + depends_on('ruby-gnuplot') + depends_on('ruby-narray') + depends_on('ruby-rubyinline') + depends_on('ruby-terminal-table') + + depends_on('python@2.6:', type=('build', 'run')) + depends_on('blast-plus') + depends_on('muscle') + depends_on('mummer') + depends_on('blat') + depends_on('vmatch') + depends_on('bowtie') + depends_on('bwa') + depends_on('usearch') + depends_on('velvet') + depends_on('idba') + depends_on('ray') + depends_on('scan-for-matches') + + def install(self, spec, prefix): + install_tree('.', prefix) + + def setup_environment(self, spack_env, run_env): + # Note: user will need to set environment variables on their own, + # dependent on where they will want data to be located: + # BP_DATA - Contains genomic data etc. + # BP_TMP - Required temporary directory + # BP_LOG - Required log directory + run_env.prepend_path('BP_DIR', prefix) |